Integrated analyses of copy number variations and gene differential expression in lung squamous-cell carcinoma.

Zhao Yang,Simin Jiang,Ying Yan,Tao Wang,Bing Zhuan

doi:10.1186/s40659-015-0038-3

Abstract

BackgroundAlthough numerous efforts have been made, the pathogenesis underlying lung squamous-cell carcinoma (SCC) remains unclear. This study aimed to identify the CNV-driven genes by an integrated analysis of both the gene differential expression and copy number variation (CNV).ResultsA higher burden of the CNVs was found in 10–50 kb length. The 16 CNV-driven genes mainly located in chr 1 and chr 3 were enriched in immune response [e.g. complement factor H (CFH) and Fc fragment of IgG, low affinity IIIa, receptor (FCGR3A)], starch and sucrose metabolism [e.g. amylase alpha 2A (AMY2A)]. Furthermore, 38 TFs were screened for the 9 CNV-driven genes and then the regulatory network was constructed, in which the GATA-binding factor 1, 2, and 3 (GATA1, GATA2, GATA3) jointly regulated the expression of TP63.ConclusionsThe above CNV-driven genes might be potential contributors to the development of lung SCC.

Highlights

Numerous efforts have been made, the pathogenesis underlying lung squamous-cell carcinoma (SCC) remains unclear
In this study we conducted an integrated analysis of transcriptional profile and copy number variation (CNV) of lung SCC, and screened 16 CNV-driven genes
The variation in these gene copy number is speculated to have a role in lung SCC occurrence

Summary

Introduction

Numerous efforts have been made, the pathogenesis underlying lung squamous-cell carcinoma (SCC) remains unclear. This study aimed to identify the CNV-driven genes by an integrated analysis of both the gene differential expression and copy number variation (CNV). Numerous efforts have been made to elucidate the underlying pathogenesis and therapy of this disease over the past few decades, lung SCC is still incurable due to lack of effective therapeutic methods and late diagnosis [5, 6]. Copy number variants (CNVs) are DNA segments of ≥1 kb in length, which is present in the genome in a Expression profile analyses have been performed to identify a mass of differentially expressed genes (DEGs) between normal and lung tumor samples.

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